LAMMPS (8 Feb 2023)
Processor partition = 3
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
variable ibead uloop 8 pad

units           real
neigh_modify    delay 2 every 1

atom_style      full
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic

pair_style      lj/charmm/coul/long 11 12
pair_modify     mix arithmetic
kspace_style    pppm 1e-4

read_data system.data
Reading data file ...
  orthogonal box = (-23.109 -22.733 -23.141) to (22.853 22.912 22.8)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  8674 atoms
  reading velocities ...
  8674 velocities
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  18 = max dihedrals/atom
  scanning impropers ...
  1 = max impropers/atom
  reading bonds ...
  5869 bonds
  reading angles ...
  3264 angles
  reading dihedrals ...
  708 dihedrals
  reading impropers ...
  38 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     4 = max # of 1-2 neighbors
     9 = max # of 1-3 neighbors
    17 = max # of 1-4 neighbors
    21 = max # of special neighbors
  special bonds CPU = 0.015 seconds
  read_data CPU = 0.153 seconds
#read_restart    system_${ibead}.rest1
special_bonds   charmm

fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0

thermo          10
thermo_style    custom step temp pe etotal f_1[1] f_1[2] f_1[3]
thermo_modify   colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
timestep        0.08

# restart         100 system_${ibead}.rest1 system_${ibead}.rest2

group prot id <= 256
256 atoms in group prot
# dump 1 prot dcd 100 prot_${ibead}.dcd

run             200
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
  G vector (1/distance) = 0.22071363
  grid = 20 20 20
  stencil order = 5
  estimated absolute RMS force accuracy = 0.024910591
  estimated relative force accuracy = 7.5017505e-05
  using double precision KISS FFT
  3d grid and FFT values/proc = 15625 8000
Generated 231 of 231 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 2 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 14
  ghost atom cutoff = 14
  binsize = 7, bins = 7 7 7
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/charmm/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
WARNING: Inconsistent image flags (src/domain.cpp:815)
Per MPI rank memory allocation (min/avg/max) = 84.59 | 84.59 | 84.59 Mbytes
   Step          Temp          PotEng         TotEng        espring         T_ring         virial    
         0   306.20099     -26166.171     -18250.089      0              0             -676.31071    
        10   23.892089     -26194.747     -25577.075      6.0651132      382.22935     -806.80519    
        20   27.051257     -26510.555     -25811.21       19.798054      432.77021     -722.7628     
        30   27.053581     -26558.283     -25858.879      46.409761      432.8074      -314.77439    
        40   19.1336       -26301.271     -25806.618      80.715535      306.1023       33.240778    
        50   19.277021     -25564.199     -25065.839      122.0411       308.39678      420.32166    
        60   20.762569     -24490.516     -23953.751      171.68786      332.16281      922.0134     
        70   18.895283     -23277.775     -22789.283      228.13302      302.28967      1340.4892    
        80   20.103678     -22119.758     -21600.026      293.69148      321.62176      1692.277     
        90   18.733051     -21236.09      -20751.793      371.14173      299.69426      2111.5887    
       100   18.287299     -20684.674     -20211.9        458.53118      292.56305      2434.0418    
       110   18.012563     -20345.727     -19880.056      560.10663      288.16778      2560.064     
       120   17.92092      -19998.225     -19534.923      676.3247       286.70167      2752.7643    
       130   17.494577     -19524.549     -19072.269      808.35795      279.88096      3081.7784    
       140   17.122298     -18815.761     -18373.106      957.14076      273.92518      3209.6451    
       150   17.447826     -17981.659     -17530.588      1123.5613      279.13303      3627.9284    
       160   17.6202       -17066.393     -16610.866      1310.1872      281.8907       4230.0427    
       170   17.370561     -16269.055     -15819.981      1507.5411      277.89693      4602.925     
       180   17.444401     -15692.511     -15241.529      1720.5033      279.07824      5000.4081    
       190   17.587192     -15476.239     -15021.565      1938.8703      281.36263      5063.6159    
       200   18.000638     -15470.948     -15005.586      2164.2187      287.977        4707.0585    
Loop time of 35.3335 on 1 procs for 200 steps with 8674 atoms

Performance: 0.039 ns/day, 613.428 hours/ns, 5.660 timesteps/s, 49.098 katom-step/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 27.094     | 27.094     | 27.094     |   0.0 | 76.68
Bond    | 0.1276     | 0.1276     | 0.1276     |   0.0 |  0.36
Kspace  | 2.3873     | 2.3873     | 2.3873     |   0.0 |  6.76
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.11312    | 0.11312    | 0.11312    |   0.0 |  0.32
Output  | 0.0020657  | 0.0020657  | 0.0020657  |   0.0 |  0.01
Modify  | 5.5507     | 5.5507     | 5.5507     |   0.0 | 15.71
Other   |            | 0.05892    |            |       |  0.17

Nlocal:           8674 ave        8674 max        8674 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          27366 ave       27366 max       27366 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    4.48585e+06 ave 4.48585e+06 max 4.48585e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 4485849
Ave neighs/atom = 517.16036
Ave special neighs/atom = 2.2573207
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:35
